Methods and systems for reading dna storage genes

Abstract

Methods and systems for use in reading DNA storage genes generally include removing one or more linking symbols from a first strand of a DNA storage gene, introducing a test symbol pool to the DNA storage gene, and replacing a data symbol in the first strand of the DNA storage gene with a single stranded test symbol from the test symbol pool when the linking symbol and data symbol of the single stranded test symbol are complimentary to an adjacent linking symbol and data symbol in the second strand of the DNA storage gene. The DNA storage gene is then scanned to identify locations on the DNA storage gene where the linking symbol is double stranded or single stranded. The locations where double stranded linking symbols are detected are then used, along with the composition of the test symbol pool, to read the DNA storage gene.

I/We claim: 
     
         1 . A method for use in reading a DNA storage gene, comprising:
 (1) removing one or more linking symbols from a first strand of a DNA storage gene;   (2) introducing a test symbol pool to the DNA storage gene, the test symbol pool comprising:
 a plurality of single stranded test symbols, each single stranded test symbol comprising a data symbol and a linking symbol; 
   (3) replacing a data symbol in the first strand of the DNA storage gene with a single stranded test symbol from the test symbol pool when the data symbol and the linking symbol in the single stranded test symbol are complimentary, respectively, to an adjacent linking symbol and data symbol in the second strand of the DNA storage gene;   (4) scanning the DNA storage gene to identify whether each linking symbol in the DNA storage gene is single stranded DNA or double stranded DNA; and   (5) recording each location on the DNA storage gene where the linking symbol is double stranded DNA.   
     
     
         2 . The method of  claim 1 , wherein the test symbol pool is a first test symbol pool and includes a set of one or more different data symbols and each data symbol included in the first test symbol pool is known. 
     
     
         3 . The method of  claim 2 , wherein steps (2)-(5) are repeated using a second test symbol pool including a set of one or more different data symbols, wherein each data symbol included in the second test symbol pool is known and wherein the set of data symbols in the second test symbol pool is different from the set of data symbols in the second test symbol pool. 
     
     
         4 . The method of  claim 3 , wherein steps (2)-(5) using the second test symbol pool is carried out concurrently with steps (2)-(5) using the first test symbol pool. 
     
     
         5 . The method of  claim 3 , wherein a combination of the recorded linking symbol locations and the known data symbols in each test pool is used to read the DNA storage gene. 
     
     
         6 . The method of  claim 1 , wherein all linking symbols are removed from the first strand of the DNA storage gene. 
     
     
         7 . The method of  claim 1 , wherein replacing data symbols in the first strand of the DNA storage gene with single stranded test symbols is carried out via toe-hold mediated strand displacement 
     
     
         8 . The method of  claim 1 , wherein the linking symbol in each single stranded test symbol is positioned at an end of the single stranded test symbol. 
     
     
         9 . The method of  claim 1 , wherein removing one or more linking symbols from the first strand of the DNA storage gene comprises:
 introducing an enzyme to the DNA storage gene, the enzyme being programmed to cut the DNA storage gene at both ends of one or more linking symbols in the DNA storage gene; and   heating the DNA storage gene to remove the one or more linking symbols from the first stand of the DNA storage gene.   
     
     
         10 . The method of  claim 1 , wherein each single stranded test symbol further comprises an anchor symbol and wherein the anchor symbol is located at one end of the single stranded test symbol and the linking symbol is located at an opposite or same end of the single stranded test symbol. 
     
     
         11 . A method for use in reading a DNA storage gene, comprising:
 (1) providing a first DNA storage gene having one or more linking symbols removed from a first strand of the DNA storage gene;   (2) introducing a first test symbol pool to the first DNA storage gene, the first test symbol pool comprising:
 a plurality of single stranded test symbols, each single stranded test symbol comprising one of a first set of data symbols and one of a first set of linking symbols; 
   (3) replacing a data symbol in the first strand of the first DNA storage gene with a single stranded test symbol from the first test symbol pool when the data symbol and the linking symbol in the single stranded test symbol are complimentary, respectively, to an adjacent linking symbol and data symbol in the second strand of the first DNA storage gene;   (4) scanning the first DNA storage gene to identify whether each linking symbol in the first DNA storage gene is single stranded DNA or double stranded DNA;   (5) recording each location on the first DNA storage gene where the linking symbol is double stranded DNA;   (6) providing a second DNA storage gene having one or more linking symbols removed from a first strand of the second DNA storage gene, the second DNA storage gene being identical to the first DNA storage gene;   (7) introducing a second test symbol pool to the second DNA storage gene, the second test symbol pool comprising:
 a plurality of single stranded test symbols, each single stranded test symbol comprising one of a second set of data symbols and one of the first set of linking symbols, the second set of data symbols being different from the first set of data symbols; 
   (8) replacing a data symbol in the second strand of the second DNA storage gene with a single stranded test symbol from the second test symbol pool when the data symbol and the linking symbol in the single stranded test symbol are complimentary, respectively, to an adjacent linking symbol and data symbol in the second strand of the second DNA storage gene;   (9) scanning the second DNA storage gene to identify whether each linking symbol in the second DNA storage gene is single stranded DNA or double stranded DNA;   (10) recording each location on the second DNA storage gene where the linking symbol is double stranded DNA; and   (11) using the recoded locations from steps (5) and (10) and the composition of the first test symbol pool and the second test symbol pool to read the DNA storage gene.   
     
     
         12 . The method of  claim 11 , wherein all linking symbols are removed from the first strand of the first DNA storage gene and the second DNA storage gene. 
     
     
         13 . The method of  claim 11 , wherein all data symbols and linking symbols in the first test symbol pool and the second test symbol pool are known. 
     
     
         14 . The method of  claim 11 , wherein replacing data symbols in the first strand of the first DNA storage gene with single stranded test symbols and replacing data symbols in the first strand of the second DNA storage gene with single stranded test symbol is carried out via toe-hold mediated strand displacement 
     
     
         15 . The method of  claim 11 , wherein the linking symbol in each single stranded test symbol is positioned at an end of the single stranded test symbol. 
     
     
         16 . The method of  claim 1 , wherein removing one or more linking symbols from the first strand of the first DNA storage gene and from the first strand of the second DNA storage gene comprises:
 introducing an enzyme to the first and second DNA storage gene, the enzyme being programmed to cut the first and second DNA storage gene at both ends of one or more linking symbols in the first and second DNA storage gene; and   heating the first and second DNA storage gene to remove the one or more linking symbols from the first stand of the first and second DNA storage gene.   
     
     
         17 . The method of  claim 11 , wherein steps (1)-(5) are carried out concurrently with steps (6)-(10). 
     
     
         18 . A system for use in reading a DNA storage gene, comprising:
 a reaction vessel configured to receive a DNA storage gene;   an enzyme source in fluid communication with the reaction vessel, the enzyme source including an enzyme configured to remove one or more linking symbols from a first strand of a DNA storage gene;   one or more test symbol pool sources, each of the one or more test symbol pool sources being in fluid communication with the reaction vessel, each of the one or more test symbol pool sources comprising a test symbol pool comprising a plurality of single stranded test symbols, each single stranded test symbol comprising a data symbol and a linking symbol; and   a scanner configured to scan a DNA storage gene located in the reaction vessel and distinguish between single stranded DNA and double stranded DNA in the DNA storage gene, detect a single stranded DNA overhang, or both.   
     
     
         19 . The system of  claim 18 , further comprising:
 a recorder configured to record each location on the DNA storage gene where the scanner identifies double stranded DNA or a single stranded DNA overhang.   
     
     
         20 . The system of  claim 19 , wherein the recorder is incorporated into the scanner.